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Bump release

Bump release #62

Workflow file for this run

.github/workflows/analytical-validation-tests.yaml at 384b154
name: tests
on:
workflow_dispatch:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
Dry_Run_and_Lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: docker://snakemake/snakemake:v5.24.2
- name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (with replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay cfChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \
/opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end cfChIP pipeline config file (with replicates, with inputs)
run: |
echo "Generated config file for cfChIP pipeline (with replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end cell-free ChIP-seq pipeline, all options (without replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay cfChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end cfChIP pipeline config file (without replicates, with inputs)
run: |
echo "Generated config file for cfChIP pipeline (without replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S2_R1.fastq.gz /opt2/.tests/Input_S2_R2.fastq.gz \
/opt2/.tests/Input_S3_1.fastq.gz /opt2/.tests/Input_S3_2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ChIP pipeline config file (with replicates, with inputs)
run: |
echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ChIP-seq pipeline, all options (with replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ChIP pipeline config file (with replicates, without inputs)
run: |
echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ChIP pipeline config file (without replicates, with inputs)
run: |
echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ChIP-seq pipeline, all options (without replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ChIP pipeline config file (without replicates, without inputs)
run: |
echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz \
/opt2/.tests/Input_S2_R1.fastq.gz \
/opt2/.tests/Input_S3_1.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the single-end ChIP pipeline config file (with replicates, with inputs)
run: |
echo "Generated config file for ChIP pipeline (with replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run single-end ChIP-seq pipeline, all options (with replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: Dry Run single-end ChIP-seq pipeline, with replicates, missing input column
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs_missing_InputControl.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the single-end ChIP pipeline config file (with replicates, without inputs)
run: |
echo "Generated config file for ChIP pipeline (with replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the single-end ChIP pipeline config file (without replicates, with inputs)
run: |
echo "Generated config file for ChIP pipeline (without replicates, with inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run single-end ChIP-seq pipeline, all options (without replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ChIP --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the single-end ChIP pipeline config file (without replicates, without inputs)
run: |
echo "Generated config file for ChIP pipeline (without replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ATAC-seq pipeline, all options (with replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ATAC --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_with_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ATAC pipeline config file (with replicates, without inputs)
run: |
echo "Generated config file for ATAC pipeline (with replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end ATAC-seq pipeline, all options (without replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay ATAC --genome hg19 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end ATAC pipeline config file (without replicates, without inputs)
run: |
echo "Generated config file for ATAC pipeline (without replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end CUT & RUN pipeline, all options (without replicates, with inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay cutnrun --genome hg38 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_with_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end CUT & RUN pipeline config file (without replicates, without inputs)
run: |
echo "Generated config file for CUT & RUN pipeline (without replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Dry Run paired-end CUT & RUN pipeline all options, all options (without replicates, without inputs)
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
/opt2/chrom-seek run --assay cutnrun --genome hg38 --input \
/opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
/opt2/.tests/Input_S1.R1.fastq.gz /opt2/.tests/Input_S1.R2.fastq.gz \
/opt2/.tests/Input_S4_R1.001.fastq.gz /opt2/.tests/Input_S4_R2.001.fastq.gz \
--output /opt2/output --peakcall /opt2/.tests/peakcall_no_replicates_no_inputs.tsv \
--contrasts /opt2/.tests/contrasts.tsv --mode local --dry-run
- name: View the paired-end CUT & RUN pipeline config file (without replicates, without inputs)
run: |
echo "Generated config file for CUT & RUN pipeline (without replicates, without inputs)...." && jq -C '.' $PWD/output/config.json
- name: Lint Workflow
continue-on-error: true
run: |
docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
unit_test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
run: python -c "import sys; print(sys.version)"
- name: Run unit tests
run: python -m unittest discover tests